Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.
Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.
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DOI：
10.1186/1471-2164-14-431
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发表时间：
2013-06-28
期刊：
影响因子：
4.4
通讯作者：
Savka MA
中科院分区：
文献类型：
--
作者：
Gan HM;Hudson AO;Rahman AY;Chan KG;Savka MA
已知属于新鞘氨醇菌属的细菌在代谢上是多功能的，并且占据不同的生态位。在缺乏基因组数据和/或分析的情况下，属于该属的细菌的知识目前仅限于生物化学特征。在这项研究中，我们分析了六种细菌的全基因组测序数据的Novosphingobium属，并提供证据表明，与耐盐性，细胞-细胞信号和芳香族化合物生物降解表型相关的基因的存在。此外，我们显示了测序的细菌之间的分类关系的基础上，基因组分析，平均氨基酸同一性（AAI）和基因组签名。新鞘氨醇菌菌株的分类聚类通常受其分离来源的影响。AAI和基因组特征为Novosphingobium sp. PP 1 Y分类为Novosphingobium pentaromaticivorans PP 1 Y提供了有力的支持。海洋新鞘氨醇菌独特的核心基因组的鉴定和随后的功能注释表明，四氢嘧啶合成可能是盐水适应的主要贡献因素。鉴定了编码N-酰基-高丝氨酸内酯（阿勒）类的细胞-细胞信号分子的合成和受体的基因。值得注意的是，在菌株PP 1 Y中发现了一个单独的luxR同源物，该同源物可能是最近通过水平基因转移获得的，这通过基因上游存在多个移动的元件而得到证实。此外，系统发育树分析和序列比较与功能验证的芳环羟化双加氧酶（ARDO）揭示了存在的几个ARDO（加氧酶）在Novosphingobium细菌与他们中的大多数属于组II和III的酶。结合对新鞘氨醇菌菌株的独特表型的先验知识和对其全基因组的荟萃分析，能够鉴定与工业应用和生物修复相关的几个基因。这种有针对性但全面的比较基因组学分析的结果有可能有助于理解属于Novosphingobium属的细菌的适应性，细胞间通讯和生物修复特性。
Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures. The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme. The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.
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影响因子：
5.6
作者：
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通讯作者：
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DOI：
10.1099/ijs.0.02301-0
发表时间：
2003-01-01
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发表时间：
2005-05-01
影响因子：
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作者：
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